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HiddenSequences now array, not hashtable
[jalview.git]
/
src
/
jalview
/
gui
/
AlignViewport.java
diff --git
a/src/jalview/gui/AlignViewport.java
b/src/jalview/gui/AlignViewport.java
index
ddb871e
..
7d02e14
100755
(executable)
--- a/
src/jalview/gui/AlignViewport.java
+++ b/
src/jalview/gui/AlignViewport.java
@@
-280,9
+280,11
@@
public class AlignViewport
{
long t = System.currentTimeMillis();
{
long t = System.currentTimeMillis();
+ int alWidth = alignment.getWidth();
+
Conservation cons = new jalview.analysis.Conservation("All",
jalview.schemes.ResidueProperties.propHash, 3,
Conservation cons = new jalview.analysis.Conservation("All",
jalview.schemes.ResidueProperties.propHash, 3,
- alignment.getSequences(), 0, alignment.getWidth() - 1);
+ alignment.getSequences(), 0, alWidth -1);
cons.calculate();
cons.verdict(false, ConsPercGaps);
cons.calculate();
cons.verdict(false, ConsPercGaps);
@@
-295,7
+297,7
@@
public class AlignViewport
System.out.println("Conservation took " + (System.currentTimeMillis() - t) +
"ms");
System.out.println("Conservation took " + (System.currentTimeMillis() - t) +
"ms");
- int alWidth = alignment.getWidth();
+
String sequence = cons.getConsSequence().getSequence();
float minR;
float minG;
String sequence = cons.getConsSequence().getSequence();
float minR;
float minG;
@@
-389,7
+391,7
@@
public class AlignViewport
if(ap!=null)
{
if(ap!=null)
{
- ap.annotationPanel.repaint();
+ ap.repaint();
}
updatingConservation = false;
}
}
updatingConservation = false;
}
@@
-523,7
+525,7
@@
public class AlignViewport
if (ap != null)
{
if (ap != null)
{
- ap.annotationPanel.repaint();
+ ap.repaint();
}
}
@@
-1439,7
+1441,7
@@
public class AlignViewport
// be done to remove redundancy.
CigarArray aligview = getViewAsCigars(selectedOnly);
if (aligview!=null) {
// be done to remove redundancy.
CigarArray aligview = getViewAsCigars(selectedOnly);
if (aligview!=null) {
- return new AlignmentView(aligview,
+ return new AlignmentView(aligview,
(selectedOnly && selectionGroup!=null) ? selectionGroup.getStartRes() : 0);
}
return null;
(selectedOnly && selectionGroup!=null) ? selectionGroup.getStartRes() : 0);
}
return null;